Can I render each layer with transparent background?
Answer to 1st question:

**Rendering an image with transparency in **BLENDER INTERNAL****


First you have to tell blender not to render the background, or sky: Under "Render/Shading", switch alpha from "sky" to "transparent". Now only the objects in the scene will be rendered.
You must render to a file format that supports transparency, such as "PNG". Under "Render/Output", switch the file format to "PNG".
Make sure the image channel setting is "RGBA", not "BW" or "RGB". The A in RGBA stands for alpha, where the transparency information is stored in the PNG file.